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     <title>Advanced Normalization Tools</title>

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            <h1 class="fn">Advanced Normalization Tools</h1>
        
            <p>
                Questions: <a
                href="http://sourceforge.net/p/advants/discussion/">Discussion
                Site</a><br />
                Email: <a class="email" href="mailto:antsr.me@gmail.com">antsr.me at gmail
                dot com</a><br />
	        Install ANTs via pre-built: <a href="http://sourceforge.net/projects/advants/files/ANTS/">Packages</a><br />
	        Build <a href="https://github.com/stnava/ANTs">ANTs</a> from: <a href="http://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/">Source-Code</a> (recommended)
           </p>
        </div>
                
        <div id="objective">
            <p>
            ANTs extracts information from
            complex datasets that include imaging (<a
            href="http://brianavants.files.wordpress.com/2013/05/avants_wordcloud.jpg">Word
            Cloud</a>).  Paired with <a
            href="http://stnava.github.com/ANTsR/">ANTsR</a> (answer),
            ANTs is useful for managing, interpreting and
            visualizing multidimensional data. ANTs is <a href="https://sourceforge.net/projects/advants/files/ANTS/stats/timeline?dates=2010-07-19+to+2099-05-25">popularly</a> considered
            a state-of-the-art medical image registration and segmentation toolkit. ANTsR is an emerging tool supporting standardized
            multimodality image analysis.  ANTs depends on the Insight
            ToolKit  <a href="http://www.itk.org">(ITK)</a>, a widely used  
            medical image processing library to which ANTs developers contribute.
            </p>
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        <div class="clear"></div>
        
        <dl>
            <dd class="clear"></dd>
            
            <dt>Authors</dt>
            <dd>
                <h2>Brian B. Avants - UPENN</h2>
                <p><strong>Role:</strong> Creator, Algorithm Design,
            Implementation, <a href="http://stnava.github.io/Resume/">more</a><br /></p>
           </dd>
           <dd>
                <h2>Nicholas J. Tustison - UVA</h2>
                <p><strong>Role:</strong> Compeller, Algorithm Design,
            Implementation Guru<br /></p>
            </dd>
	     <dd>
               <p><strong>Team:</strong> Gang Song (Originator),
            Jeffrey T. Duda (DTI), Hans J. Johnson (Large-Scale
            Application, Testing)<br /></p>
            </dd>
            <dd class="clear"></dd>
            
            <dt>Methods References</dt>
            <dd>
                <h2>Image Registration</h2>
                <p>Diffeomorphisms: <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/17659998">SyN</a>,
            Independent Evaluation: <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/19195496">Klein</a>,
	      <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/21632295">Murphy</a>,
	      Template Construction
	      <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/15501083">(2004)</a><a
            href="http://www.ncbi.nlm.nih.gov/pubmed/19818860"> (2010)</a>,
	      <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/20851191">Similarity
            Metrics</a>,
	      <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/18995188">Multivariate
            registration</a>,
	      <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/23151955">Multiple
            modality analysis and statistical bias</a>
            </p>
               <h2>Image Segmentation</h2>
                <p>Atropos Multivar-EM Segmentation <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/21373993">(link)</a>,
            Multi-atlas methods <a href="http://www.ncbi.nlm.nih.gov/pubmed/21237273N4">(link)</a>, Bias
                Correction <a
                href="http://www.ncbi.nlm.nih.gov/pubmed/20378467">(link)</a>,
                DiReCT cortical thickness <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/19150502">(link)</a>,
            DiReCT in
            <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/23516289">chimpanzees</a>
            </p>
	      
	      <h2>Multivariate Analysis <span>Eigenanatomy <a
                href="http://www.ncbi.nlm.nih.gov/pubmed/23286132">(1)</a>
                <a
                href="http://www.ncbi.nlm.nih.gov/pubmed/23475817">(2)</a>
                </span></h2>
                <p>Prior-Based Eigenanatomy <a
                href="http://www.ncbi.nlm.nih.gov/pubmed/?">(in
                prep)</a>,
                Sparse CCA <a
                href="http://www.ncbi.nlm.nih.gov/pubmed/20083207">(1)</a>,
	      <a
                href="http://www.ncbi.nlm.nih.gov/pubmed/20879247">(2)</a>,
                Sparse Regression <a
                href="http://link.springer.com/chapter/10.1007%2F978-3-642-38868-2_8">(link)</a>
                </p>

	      <h2>ImageMath <span>Useful!</span></h2>
                <p>morphology, GetLargestComponent, CCA, FillHoles
                ... much more!</p>
          </dd>
            
            <dd class="clear"></dd>
            
            <dt>Application Domains</dt>
            <dd>
	       <h2>Frontotemporal degeneration <span><a href="http://ftd.med.upenn.edu">PENN
            FTD center</a></span>
               <h2>Neuroimaging <span>Multimodality</span></h2>
                <ul>
                    <li>Structural MRI</li>
                    <li>Functional MRI</li>
                    <li>Network Analysis</li>
                </ul> 
               <h2>Lung imaging <span>Translational</span></h2>
                <ul>
                    <li>Structure</li>
                    <li>Perfusion MRI</li>
                    <li>Branching</li>
                </ul> 
           </dd>

	    <dd class="clear"></dd>
 
            <dt>Background & Theory</dt>
            <dd>
               <ul>
		 <li>The <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22SyN%22)+AND+%22Avants+B%22">
            SyN</a> and <a
            href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22N4%22)+AND+%22Tustison+N4ITK%22">
            N4 bias correction</a> papers and other relevant references in <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22Tustison+N%22)+AND+%22Avants+B%22">Pubmed</a></li>            
		 <li>Visualization: e.g. <a href="http://vimeo.com/66781467">a gource of ANTs development</a></li>
                 <li><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22DIRECT%22)+AND+%22Avants%22+AND+DAS">DiReCT</a> cortical thickness <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=((%22Cortical+Thickness%22)+AND+%22Avants%22">papers</a></li>
		 
		   <li>A <a
            href="https://sourceforge.net/projects/advants/files/Documentation/">folder</a>
            of relevant docs: <a
            href="http://sourceforge.net/projects/advants/files/Documentation/atropos.pdf/download">segmentation</a>,
            <a
            href="http://sourceforge.net/projects/advants/files/Documentation/antstheory.pdf/download">registration</a>,
            <a
            href="http://sourceforge.net/projects/advants/files/Documentation/ants.pdf/download">usage(old)</a>,
            <a
            href="http://sourceforge.net/projects/advants/files/Documentation/ANTSMethodologySummary.docx/download">for
            clinical apps</a></li>
                   <li>ANTs redesigned for generality, automation,
                multi-core computation with ITKv4</li>
                    <li>Dev'd ITKv4 with Kitware, GE, Natl. Lib of
                Medicine & Academia</li>
               </ul>
            </dd>

	    <dd class="clear"></dd>
 
            <dt>Acclaim for Robustness & Other News</dt>
            <dd>
	       <h2>ANTs has won several competitions<span>
	         Unbiased & international</span></h2>
                <ul>
                   <li>New <i>antsRegistration</i> <a href="https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh">bash example</a></li>
                   <li>New <i>Eigenanatomy</i> for <a
	         href="http://www.ncbi</a>.nlm.nih.gov/pubmed/23269595">multivariate
	         neuroimage analysis</a> via <a
	         href="http://www.ncbi.nlm.nih.gov/pubmed/23286132">PCA</a> &
	         <a href="http://www.ncbi.nlm.nih.gov/pubmed/20083207">CCA</a> </a></li>
                    <li>ANTs finished in 1st rank in <a href="http://www.ncbi.nlm.nih.gov/pubmed/19195496">Klein
	         2009 intl. brain mapping competition</a></li>
                    <li>ANTs finished 1st overall in <a href="http://www.ncbi.nlm.nih.gov/pubmed/21632295">
	         EMPIRE10 intl. lung mapping competition</a></li>
                    <li>ANTs is the standard registration for
	         <a href="http://www.miccai2013.org/">MICCAI-2013</a> segmentation competitions</li>
                    <li>Conducting ANTs-based R tutorial @ MICCAI-2013</li>
                    <li>ITK-focused Frontiers in
	         Neuroinformatics research topic <a href="http://www.frontiersin.org/neuroinformatics/researchtopics/neuroinformatics_with_the_insi/1580">here</a></li>
               </ul>
          </dd>
            
            <dd class="clear"></dd>
            
            <dt>Learning about ANTs</dt>
            <dd>
	      <li>Presentations: e.g. <a
	      href="http://prezi.com/mwrmcm-h9-w4/ants/?kw=view-mwrmcm-h9-w4&rc=ref-40024395">a
	      Prezi about ANTs</a> (WIP)</li>
	      <li>Reproducible science as a teaching tool: e.g. <a
	      href="https://github.com/stnava/ANTS_MultiModality"> compilable ANTs tutorial</a> (WIP)</li>
	      <li>Other examples <a
	      href="http://brianavants.wordpress.com"> slideshow</a> </li>
              <li>Landmark-based mapping for e.g. hippocampus <a
            href="https://sourceforge.net/p/advants/discussion/840261/thread/1cb7b165/?limit=50">
            discussed here</a></li>
	    <li>Brief ANTs segmentation <a href="http://vimeo.com/67814201"> video</a></li>
	    </dd>

            <dd class="clear"></dd>
            
            <dt>References</dt>
            <dd><li><a href="http://scholar.google.com/scholar?q=Advanced+Normalization+Tools+%22ANTs%22+-ant&hl=en&as_sdt=1%2C39&as_ylo=2008&as_yhi=">Google Scholar</a></li>            
            <li><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=(%22Avants%20B%22)%20OR%20%22Tustison%20N%22">Pubmed</a></li>            
            <li>ANTs was supported by: R01-EB006266-01</li>
            <dd class="clear"></dd>
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